mapping performance improvement

source/ErrorWarning.cpp

@@ -5,7 +5,7 @@
 #include "TimeFunctions.h"
 #include "GlobalVariables.h"
 
-void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, Parameters &P) {
+void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, const Parameters &P) {
     time_t timeCurrent;
     time( &timeCurrent);
     if (P.runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexError);
@@ -30,4 +30,4 @@ void warningMessage(string messageOut, ostream &streamOut1, ostream &streamOut2,
     if (streamOut2.good()) {
         streamOut2 << "WARNING: " << messageOut << "\t\t " << timeMonthDayTime(timeCurrent) <<endl;
     };
-};
+};

source/ErrorWarning.h

@@ -4,6 +4,6 @@
 #include "IncludeDefine.h"
 #include "Parameters.h"
 
-void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, Parameters &P);
+void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, const Parameters &P);
 void warningMessage(string messageOut, ostream &streamOut1, ostream &streamOut2, Parameters &P);
 #endif

source/ReadAlign_assignAlignToWindow.cpp

@@ -13,10 +13,15 @@ void ReadAlign::assignAlignToWindow(uint a1, uint aLength, uint aStr, uint aNrep
     {//do not check for overlap if this is an sj-align
         uint iA;
         for (iA=0; iA<nWA[iW]; iA++) {
-            if (aFrag==WA[iW][iA][WA_iFrag] && WA[iW][iA][WA_sjA]==sjA \
-                && a1+WA[iW][iA][WA_rStart]==WA[iW][iA][WA_gStart]+aRstart \
-                && ( (aRstart>=WA[iW][iA][WA_rStart] && aRstart<WA[iW][iA][WA_rStart]+WA[iW][iA][WA_Length]) \
-                  || (aRstart+aLength>=WA[iW][iA][WA_rStart] && aRstart+aLength<WA[iW][iA][WA_rStart]+WA[iW][iA][WA_Length]) ) ) {//this piece overlaps with iA
+          auto& align = WA[iW][iA];
+          if (a1+align[WA_rStart]==align[WA_gStart]+aRstart
+              && aFrag==align[WA_iFrag]
+              && align[WA_sjA]==sjA
+              && ((aRstart >= align[WA_rStart] &&
+                    aRstart < align[WA_rStart]+align[WA_Length])
+                   || (aRstart+aLength>=align[WA_rStart]
+                       && aRstart+aLength<align[WA_rStart]+align[WA_Length]))) {
+            //this piece overlaps with iA
                 break;
             };
         };

source/ReadAlign_outputTranscriptSAM.cpp

@@ -232,7 +232,7 @@ uint ReadAlign::outputTranscriptSAM(Transcript const &trOut, uint nTrOut, uint i
         } else if (mateChr<mapGen.nChrReal){//mateChr is given in the function parameters
             *outStream <<"\t"<< mapGen.chrName[mateChr] <<"\t"<< mateStart+1-mapGen.chrStart[mateChr] <<"\t"<< 0;
         } else {
-            *outStream <<"\t"<< "*" <<"\t"<< 0 <<"\t"<< 0;
+            *outStream << "\t*\t0\t0";
         };
 
 

source/Transcript.h

@@ -64,7 +64,7 @@ class Transcript {
     void resetMapG(uint); // reset map to 0 for Lread bases
     void add(Transcript*); // add
     intScore alignScore(char **Read1, char *G, Parameters &P);
-    int variationAdjust(const Genome &mapGen, char *R);
+    int variationAdjust(const Genome &mapGen, const char *R);
     string generateCigarP(); //generates CIGAR
     void peOverlapSEtoPE(uint* mSta, Transcript &t);
     void extractSpliceJunctions(vector<array<uint64,2>> &sjOut, bool &annotYes);

source/Transcript_variationAdjust.cpp

@@ -1,7 +1,7 @@
 #include "Transcript.h"
 #include "serviceFuns.cpp"
 
-int Transcript::variationAdjust(const Genome &mapGen, char *R)
+int Transcript::variationAdjust(const Genome &mapGen, const char *R)
 {
     Variation &Var=*mapGen.Var;
 

source/extendAlign.cpp

@@ -3,7 +3,7 @@
 #include "Transcript.h"
 #include "extendAlign.h"
 
-bool extendAlign( char* R, char* G, uint rStart, uint gStart, int dR, int dG, uint L, uint Lprev, uint nMMprev, uint nMMmax, double pMMmax, bool extendToEnd, Transcript* trA ) {
+bool extendAlign(const char* R, const char* G, uint rStart, uint gStart, int dR, int dG, uint L, uint Lprev, uint nMMprev, uint nMMmax, double pMMmax, bool extendToEnd, Transcript* trA ) {
 
 // find the maximum score
 

source/extendAlign.h

@@ -2,5 +2,5 @@
 #include "Parameters.h"
 #include "Transcript.h"
 
-bool extendAlign( char* R, char* G, uint rStart, uint gStart, int dR, int dG, uint L, uint Lprev, uint nMMprev, uint nMMmax, double pMMmax, bool extendToEnd, Transcript* trA );
+bool extendAlign(const char* R, const char* G, uint rStart, uint gStart, int dR, int dG, uint L, uint Lprev, uint nMMprev, uint nMMmax, double pMMmax, bool extendToEnd, Transcript* trA );
 

source/stitchAlignToTranscript.cpp

@@ -6,7 +6,10 @@
 // #include "stitchGapIndel.cpp"
 
 
-intScore stitchAlignToTranscript(uint rAend, uint gAend, uint rBstart, uint gBstart, uint L, uint iFragB, uint sjAB, Parameters& P, char* R, Genome &mapGen, Transcript *trA, const uint outFilterMismatchNmaxTotal) {
+intScore stitchAlignToTranscript(uint rAend, uint gAend, uint rBstart,
+                                 uint gBstart, uint L, uint iFragB, uint sjAB,
+                                 const Parameters& P, const char* R, const Genome &mapGen,
+                                 Transcript *trA, const uint outFilterMismatchNmaxTotal) {
     //stitch together A and B, extend in the gap, returns max score
 
     if (trA->nExons>=MAX_N_EXONS)

source/stitchAlignToTranscript.h

@@ -1,7 +1,10 @@
+#include "Genome.h"
 #include "IncludeDefine.h"
 #include "Parameters.h"
 #include "Transcript.h"
-#include "Genome.h"
-
-intScore stitchAlignToTranscript(uint rAend, uint gAend, uint rBstart, uint gBstart, uint L, uint iFragB, uint sjAB, Parameters& P, char* R, Genome &mapGen,  Transcript *trA, uint outFilterMismatchNmaxTotal);
 
+intScore stitchAlignToTranscript(uint rAend, uint gAend, uint rBstart,
+                                 uint gBstart, uint L, uint iFragB, uint sjAB,
+                                 const Parameters &P, const char *R,
+                                 const Genome &mapGen, Transcript *trA,
+                                 uint outFilterMismatchNmaxTotal);